macOS
Homebrew已验证 · 100%
brew install flyelocal Homebrew formula metadata
安装
其他安装命令
Linux
Nix已验证 · 92%
nix profile install nixpkgs#flyenixpkgs package indexes · pkgs/by-name/fl/flye/package.nix · 来源: api.github.com
概览
软件包摘要
De novo assembler for single molecule sequencing reads using repeat graphs
历史
项目历史与用法
Flye is a de novo assembler for long, single-molecule sequencing reads from platforms such as PacBio and Oxford Nanopore. It is distributed as a command-line bioinformatics package and presents a complete assembly pipeline from raw reads to polished contigs, with special support for metagenome assembly through metaFlye.
项目历史
The project grew out of the ABruijn/Flye line of assemblers developed in Pavel Pevzner's lab at UCSD. Its official release history shows early releases under the ABruijn name in 2016 and 2017, followed by Flye releases from the 2.x series onward.
Flye's core technical identity is its repeat graph approach. The README describes repeat graphs as an alternative to de Bruijn graphs for noisy long-read data, using approximate sequence matches and classifying graph edges as unique or repetitive to support reconstruction of assemblies.
采用历史
Flye became a standard packaged long-read assembler in bioinformatics workflows because it targets both PacBio and Oxford Nanopore reads, covers bacterial through mammalian-scale assemblies, and advertises Bioconda installation from the official README. The input package metadata also records packaging across Homebrew, Debian, Ubuntu, and Nix.
使用方式
Typical usage is as the `flye` CLI: users provide raw PacBio or ONT reads, select the appropriate read mode, and receive polished contigs and graph outputs. The README also documents metagenome assembly, benchmark datasets, and downstream visualization or phasing tools.
为什么软件包爱好者会关心
Flye is notable to package maintainers because it combines Python/C++ bioinformatics code with bundled third-party components such as minimap2 and samtools, while remaining a user-facing CLI. It is also a good example of a research tool that crossed into routine package-manager distribution because long-read sequencing became common laboratory infrastructure.
时间线
- 2016: ABruijn v1.0 was released.
- 2018: The 2.3 release line appeared under the Flye name.
- 2019: The Flye repeat-graph assembler paper was published in Nature Biotechnology.
- 2020: metaFlye for long-read metagenome assembly was published in Nature Methods.
- 2021: Flye 2.9 added updated high-quality Nanopore and HiFi behavior and other assembly improvements.
- 2025: Flye 2.9.6 was released as a minor fix release.
Related projects
- Related projects named by the official README include metaFlye, HapDup, strainy, AGB, Bandage, minimap2, and samtools.
来源
安全态势
风险级别：绿色
narrow executable package without higher-risk signals.
风险分类器
绿色 风险 · 低 置信度 · appliance
原因
- narrow executable package without higher-risk signals
信号
- metadata:no-higher-risk-signals
安装行为
- formula 元数据中未记录 Homebrew post-install 钩子。
- Homebrew bottle 元数据适用于 6 个平台目标。
- 安装时包含 2 个运行时依赖。
建议审查
在无人值守的代理使用前，请检查该工具是否读取明文凭据、写入远程状态、发布制品或调用插件。
可执行文件
已安装的可执行文件
| 命令 | 类型 | 暴露范围 | 备注 |
|---|---|---|---|
flye | cli | 全局可执行文件 | |
flye-minimap2 | cli | 全局可执行文件 | |
flye-modules | cli | 全局可执行文件 | |
flye-samtools | cli | 全局可执行文件 |
新鲜度
版本和新鲜度
这些信号区分页生成时间、软件包管理器活动和上游发布比较。只有存在证据 URL 和可比较版本时，才会提示版本落后。
页面生成时间2026-07-10
管理器版本2.9.6
管理器更新时间2026-06-22
本地数据OK
上游当前
检测到的最新版本2.9.6
https://github.com/mikolmogorov/Flye
- OK没有生成新鲜度警告。
安装元数据
软件包元数据
| 软件包键 | brew:flye |
|---|---|
| 版本 | 2.9.6 |
| 软件包管理器 | Homebrew |
| 软件包管理器页面 | https://formulae.brew.sh/formula/flye |
| 主页 | https://github.com/mikolmogorov/Flye |
| 仓库 | https://github.com/mikolmogorov/Flye |
| 上游文档 | https://github.com/mikolmogorov/Flye |
| 许可证 | BSD-3-Clause AND Apache-2.0 AND BSL-1.0 AND CC-BY-3.0 AND MIT |
| 源码归档 | https://github.com/mikolmogorov/Flye/archive/refs/tags/2.9.6.tar.gz |
| 最后更新 | 2026-06-22T14:03:21-07:00 |
| Pulse | updated |
| 依赖 | python@3.14, samtools |
| Bottle | 可用 (于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | 未定义 |
| 服务 | 未声明 |
注册表事实
源数据库详情
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | flye |
| Version Scheme | 0 |
| Revision | 0 |
| Head Version | HEAD |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
源数据库匹配
其他软件包管理器记录
匹配项来自外部软件包管理器索引，并与本地 Automic Vault 软件包链接分开显示。
Debian apt95%
flye 2.9.5+dfsg-1
de novo assembler for single molecule sequencing reads using repeat graphs
https://github.com/fenderglass/Flye
sudo apt install flye- Section: science
- Architecture: amd64
- 8 依赖
- normalized package name match
- 匹配方式：Flye
Nix95%
flye
nix profile install nixpkgs#flye- normalized package name match
- 匹配方式：Flye
Ubuntu apt95%
flye 2.9.3+dfsg2-1
de novo assembler for single molecule sequencing reads using repeat graphs
https://github.com/fenderglass/Flye
sudo apt install flye- Section: universe/science
- Architecture: amd64
- 8 依赖
- normalized package name match
- 匹配方式：Flye
来源线索
由仓库数据生成
此页面由 av-web 从 scripts/generate-pkg-sqlite.py 生成的私有软件包 SQLite 工件提供。
Combined YAML source
View the package source record on GitHub.
使用的来源
- Geiger risk classifier
- Nucleus package database
- av.db category and tag curation
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- package relationship graph
- package version freshness
- package-page enrichment